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With the top down, is the door glass aligned with the 1/4 window glass better, or no? I'm wondering if something is out of whack with the convertible top frame or weatherstripping, but only because there is not really any adjustment within the regulator or elsewhere in the door.

Only thing within the door I can think of is, if you remove the door panel and then the inner side glass weatherstrip, directly beneath that weatherstrip there are two bolts (one toward the front and another toward the rear of the door) that hold the glass stabilizers. If those have somehow come loose, the glass will not be held firmly in the door and will "flop around" for lack of better term (usually noticeable by the door not sounding solid when you close it).

All you can really do then, failing an expert of sorts popping in on this thread, is take the door panel off and start looking at things. If you have to, remove the passenger side door panel (I assume the glass over there lines up as it should) as well just so you can have something else to look at as comparison. Like I said though, the only thing I can think of that might have any effect on the glass like you're experiencing is those stabilizers at the top of the door beneath the inner weatherstrip.

The passenger side shuts good. I will pull the door panel off and look inside there and see if there is anything loose or that looks out of place or broke. I will take some pictures and post my findings. Hopefully no ole else has this problem but if they do maybe I can help them after I figure it out.

Ok, from what I can tell is the back window is not going up far enough. there is an 1/8 of a in difference between how high the passenger side go up and the driver side. Is there a way to adjust the rear window? I hate to rip it all apart and there be no way to adjust it.

Yes, the window glass is adjustable. I did this recently on my wifey’s ’98 vert after replacing the window glass, regulator and door hinge pins. Take the door panel, inner window weather stripping and the vapor barrier sheet (be careful not to rip it) off the door. There are four 11mm or 12mm bolts with matching brackets in the door that control the in/out of the glass as it slides & how high up the glass goes. The bolts/brackets that control the in/out of the door are on top of the door and were covered by the inner weather stripping. One towards the front and one towards the back of the door. The bolts/brackets that control how high the window goes are in little recessed areas an inch or so below the top of the door. One in the front and one in the back (near the upper left corner of the door if your sitting in the drivers seat). Loosen all 4 bolts but don’t remove them. You want the brackets to be loose and slide easily. You may need to lower the door a little to get the brackets to loosen.

Now, with all 4 bolts loose and the window lowered a little get in the car and close the door. First you adjust the in/out of the window. Slowly raise the glass till it stops and seats in the ‘verts weather stripping. Making sure the brackets at the top of the door slide into the hooks on the window glass. Now tighten all 4 bolts. Then open/close the door a couple times paying close attention to the window glass and the ‘vert weather stripping. Make sure the window glass isn’t binding/catching on the weather stripping. If it is, lower the glass a little and barely loosen the bolts in the recessed areas in the door. Then lightly nudge them down a little and tighten them back up. Raise the window again and retest. repeat as often as necessary till you get the window aligned properly. It took me about 5 minutes to get it right on my wifey’s ride.

Now, my above post assumes that it is the main door window glass that is out of alignment. It is hard to tell from the photo’s, but the rear quarter window may be the problem here. If the main window glass seals nicely against the ‘vert top weather stripping then its alignment may be just fine. Which would point to the quarter window as the problem. There are similar adjusting bolts/brackets for the rear quarter window that you should check out. It may be that the rear window isn’t sliding up all the way and could be binding/blocked on something. Good luck...

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